Issues with running the workflow with toil-cwl-runner but not with cwltool

CWL Questions
1

Hi we tried to run the workflow at the repository:

If we run the workflow with cwltool using the job description in:

with cwltool everything works. But when we run it with toil-cwl-runner we get an error:

WARNING:toil.leader:h/Z/job39e5364q      File "<string>", line 1, in <module>
WARNING:toil.leader:h/Z/job39e5364q    cwltool.errors.WorkflowException:      steps/DP3.GenericStep.cwl:11:5: Missing required input parameter 'parameters_input'

The cwltool version is 1.0.20190906054215 while toil version is 3.21.0a1.

How is that possible?
Does it have to do with the concatenation of the JSON output?

2

Hello @Mattia_Mancini and thanks for talking to us here.

toil-cwl-runner currently has some bugs with default values and I think you have also hit the same bug

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3

Thanks, we were able to work around this bug.

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